• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.130-136
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• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• Magazine of the Korean Society of Agricultural Engineers
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• v.34 no.E
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• pp.45-59
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• 1992

At downstream part of the hydraulic structures such as spiliway or drainage gate, jet flow can occur by gate opening. If stream bed is not hard or bed protection is not sufficient, scour hole will be formed due to high shear stress of the jet flow. We call this primary scour. Once the scour hole is formed, a vortex occurs in it and this vortex causes additional scour. We call this secondary scour. The primary scour proceeds to downstream together with flow direction but the secondary one proceeds to upstream direction opposite to it. If the secondary one continues and reaches to the hydraulic structure, it can undermine the bottom of hydraulic structure and this will lead to failure of structure itself. Thus, it is necessary to know the physical features of the vortex structure in a scour hole, which is the main mechanism of the secondary scour. This study deals with the characteristics of the vortex structure and its shear stress which causes the secondary scour.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.36-40
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• 2014

Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.

• Proceedings of the KSRS Conference
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• 2005.10a
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• pp.280-282
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved algorithm provides better levels of performance than the originals.

• Earthquakes and Structures
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• v.16 no.4
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• pp.401-413
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• 2019

The concept of base isolation for equipment is well known. Its application in buildings and structures is rather challenging. Introduction of horizontal flexibility at the base helps in proper energy dissipation at the base level thus reducing the seismic demand of the super structure to be considered during design. The present study shows the results of a series of numerical simulation studies on seismic responses of secondary system (SS) housed in non-isolated and base-isolated primary structures (PS) including equipment-structure interactions. For this study the primary structure consists of two similar single bay three-store reinforced cement concrete (RCC) Frame building, one non-isolated with conventional foundation and another base isolated with Lead plug bearings (LPB) constructed at IIT Guwahati, while the secondary system is modeled as a steel frame. Time period of the base isolated building is higher than the fixed building. Due to the presence of isolator, Acceleration response is significantly reduced in both (X and Y) direction of Building. It have been found that when compared to fixed base building, the base isolated building gives better performance in high seismic prone areas.

• Journal of Positioning, Navigation, and Timing
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• v.10 no.4
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• pp.307-313
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• 2021

Modernized GNSS signal structures tend to use tiered codes, and all GNSSs use binary codes as secondary codes. However, recently, signals using polyphase codes such as Zadoff-Chu sequence have been proposed, and are expected to be utilized in GNSS. For example, there is Tiered Differential Polyphase Code (TDPC) using polyphase code as secondary code. In TDPC, the phase of secondary code changes every one period of the primary code and a time-variant error is added to the carrier tracking error, so carrier tracking ambiguity exists until the secondary code phase is found. Since the carrier tracking ambiguity cannot be solved using the general GNSS receiver architecture, a new receiver architecture is required. Therefore, in this paper, we describe the carrier tracking ambiguity and its cause in signal tracking, and propose a receiver structure that can solve it. In order to prove the proposed receiver structure, we provide three signal tracking results. The first is the differential decoding result (secondary code sync) using the general GNSS receiver structure and the proposed receiver structure. The second is the IQ diagram before and after multiplying the secondary code demodulation when carrier tracking ambiguity is solved using the proposed receiver structure. The third is the carrier tracking result of the legacy GPS (L1 C/A) signal and the signal using TDPC.

• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Proceedings of the Korea Information Processing Society Conference
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• 2005.11a
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• pp.15-18
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved prediction algorithm provides better levels of performance than the originals.

• Earthquakes and Structures
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• v.15 no.5
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• pp.565-581
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• 2018

This paper proposes a new analytical formulation for computing the seismic input at various levels of a structure in terms of floor response spectra. The approach, which neglects the dynamic interaction between primary structure and secondary element, is particularly useful for the seismic assessment of secondary and non-structural elements. The proposed formulation has a robust theoretical basis and it is based on few meaningful dynamic parameters of the main building. The method has been validated in the linear and nonlinear behavior of the main building through results coming from both experimental tests (available in literature) and parametric numerical analyses. The conditions, for which the Floor Spectrum Approach and its simplified assumptions are valid, have been derived in terms of specific interval ratios between the mass of the secondary element and the participant mass of the main structure. Finally, a practice-oriented formulation has been derived, which could be easily implementable also at code level.

• Journal of Life Science
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• v.23 no.10
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• pp.1260-1266
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• 2013

The ribosomal DNA (rDNA) clusters of Hypsizygus marmoreus 3-10 and H. marmoreus 1-1 were analyzed in this study. The small subunit (SSU) and intergenic spacer 2 (IGS 2) was partially sequenced. The internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), and 5S were completely sequenced. The rDNA clusters of H. marmoreus 3-10 and H. marmoreus 1-1 were 7,049 bp in length. The sequence of SSU rDNA, which corresponded to 18S rDNA, was 1,796 bp in length, and the sequence of LSU rDNA, which corresponded to 28S rDNA, was 3,348 bp in length. The ITS region that variable region and IGS region that non-transcribed spacer was 462 bp and 1,290 bp in length. The sequence of 5.8S rDNA and 5S rDNA was 153 bp and 43 bp in length, respectively. The 17 bp of the rDNA cluster in the H. marmoreus 3-10 strain was different to that in the H. marmoreus 1-1 strain, with 2 bp in the SSU, 3 bp in the ITS, 9 bp in the LSU, and 3 bp in the IGS. The analysis of the secondary structure revealed that the ITS regions of H. marmoreus 3-10 and H. marmoreus 1-1 have five stem-loop structures. Interestingly, among these structures, one different nucleotide sequence resulted in a different secondary structure in stem-loop V.